The impact and origin of copy number variations in the Oryza species.

Bai, Z; Chen, J; Liao, Y; Wang, M; Liu, R; Ge, S; Wing, RA; Chen, M

BMC genomics 2016

PMID: 27025496

The impact and origin of copy number variations in the Oryza species.

BACKGROUND: Copy number variation (CNV), a complex genomic rearrangement, has been extensively studied in humans and other organisms. In plants, CNVs of several genes were found to be responsible for various important traits; however, the cause and consequence of CNVs remains largely unknown. Recently released next-generation sequencing (NGS) data provide an opportunity for a genome-wide study of CNVs in rice. RESULTS: Here, by an NGS-based approach, we generated a CNV map comprising 9,196 deletions compared to the reference genome 'Nipponbare'. Using Oryza glaberrima as the outgroup, 80% of the CNV events turned out to be insertions in Nipponbare. There were 2,806 annotated genes affected by these CNV events. We experimentally validated 28 functional CNV genes including s='term' data-tid='1172' href='#term-1172'>term' data-tid='1171' href='#term-1171'>OsMADS56, BPH14, OsDCL2b and OsMADS30, implying that CNVs might have contributed to phenotypic variations in rice. Most CNV genes were found to be located in non-co-linear positions by comparison to O. glaberrima. One of the origins of these non-co-linear genes was genomic duplications caused by transposon activity or double-strand break repair. Comprehensive analysis of mutation mechanisms suggested an abundance of CNVs formed by non-homologous end-joining and mobile element insertion. CONCLUSIONS: This study showed the impact and origin of copy number variations in rice on a genomic scale.